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Zinc in PDB 4rvw: Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc)

Protein crystallography data

The structure of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc), PDB code: 4rvw was solved by C.Calmettes, T.F.Moraes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.54 / 4.48
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.548, 149.592, 157.590, 90.00, 90.00, 90.00
R / Rfree (%) 31.7 / 38

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc) (pdb code 4rvw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc), PDB code: 4rvw:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4rvw

Go back to Zinc Binding Sites List in 4rvw
Zinc binding site 1 out of 3 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:0.1
occ:1.00
NE2 A:HIS499 1.8 0.5 1.0
OE2 A:GLU340 1.9 0.1 1.0
NE2 A:HIS100 2.0 0.6 1.0
CE1 A:HIS499 2.5 0.3 1.0
CE1 A:HIS100 2.9 0.3 1.0
CD2 A:HIS100 2.9 0.4 1.0
CD A:GLU340 3.0 0.5 1.0
CD2 A:HIS499 3.0 0.4 1.0
OD1 A:ASP99 3.1 0.4 1.0
OD2 A:ASP99 3.7 0.2 1.0
OE1 A:GLU340 3.7 0.3 1.0
OG A:SER97 3.7 0.1 1.0
ND1 A:HIS499 3.8 0.6 1.0
CG A:ASP99 3.8 0.0 1.0
ND1 A:HIS100 3.9 0.1 1.0
NE2 A:HIS338 3.9 0.7 1.0
CG A:HIS100 3.9 0.9 1.0
CG A:HIS499 4.0 0.0 1.0
CG A:GLU340 4.1 0.7 1.0
CZ A:PHE350 4.2 0.8 1.0
CE1 A:PHE350 4.3 0.0 1.0
CB A:ALA501 4.3 0.5 1.0
CE1 A:HIS338 4.6 0.6 1.0
CE2 A:PHE350 4.9 0.9 1.0
CB A:SER97 5.0 0.6 1.0
CD2 A:HIS338 5.0 0.1 1.0

Zinc binding site 2 out of 3 in 4rvw

Go back to Zinc Binding Sites List in 4rvw
Zinc binding site 2 out of 3 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:0.8
occ:1.00
ND1 A:HIS87 2.2 0.3 1.0
NE2 A:HIS86 2.6 0.4 1.0
CE1 A:HIS87 2.6 0.7 1.0
NE2 A:HIS330 2.8 0.3 1.0
CD2 A:HIS86 3.2 0.9 1.0
CE1 A:HIS330 3.3 0.5 1.0
CG A:HIS87 3.5 1.0 1.0
CE1 A:HIS86 3.6 0.6 1.0
OE2 A:GLU141 3.7 0.4 1.0
CD2 A:HIS330 3.9 0.9 1.0
NE2 A:HIS87 3.9 0.4 1.0
CB A:HIS87 4.2 0.5 1.0
CD2 A:HIS87 4.3 0.7 1.0
CG A:HIS86 4.4 0.1 1.0
NH2 A:ARG328 4.4 0.5 1.0
ND1 A:HIS330 4.4 0.5 1.0
ND1 A:HIS86 4.5 0.3 1.0
CD A:ARG314 4.7 0.0 1.0
CD A:GLU141 4.7 0.7 1.0
NE A:ARG328 4.7 0.1 1.0
CZ A:ARG328 4.7 0.7 1.0
CZ A:PHE224 4.7 0.3 1.0
CG A:HIS330 4.7 0.6 1.0
OE2 A:GLU316 4.8 0.1 1.0
OE1 A:GLU141 4.9 0.8 1.0

Zinc binding site 3 out of 3 in 4rvw

Go back to Zinc Binding Sites List in 4rvw
Zinc binding site 3 out of 3 in the Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Bacterial Zn-Transporter Znud From Neisseria Meningitidis (Soaked with 20 Micromolar Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn803

b:0.6
occ:1.00
NE2 A:HIS496 2.5 0.9 1.0
CE1 A:HIS496 3.0 0.1 1.0
CD2 A:HIS496 3.4 1.0 1.0
ND1 A:HIS496 3.9 0.8 1.0
NE2 A:GLN394 3.9 1.0 1.0
CG A:HIS496 4.1 0.2 1.0
NH2 A:ARG555 4.5 0.1 1.0

Reference:

C.Calmettes, C.Ing, C.M.Buckwalter, M.El Bakkouri, C.Chieh-Lin Lai, A.Pogoutse, S.D.Gray-Owen, R.Pomes, T.F.Moraes. The Molecular Mechanism of Zinc Acquisition By the Neisserial Outer-Membrane Transporter Znud. Nat Commun V. 6 7996 2015.
ISSN: ESSN 2041-1723
PubMed: 26282243
DOI: 10.1038/NCOMMS8996
Page generated: Wed Dec 16 05:46:31 2020

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